Ab initio phasing starting from low resolution

Zeitschrift fur Kristallographie

Volumn 217, Issue 12, 2002, Pages 668-685

  Lunin, V Y ^a   Lunina, N ^a   Podjarnyn, A ^b   Bockmayr, A ^c   Urzhumtsev, A ^c  

^a INSTITUTE OF MATHEMATICAL PROBLEMS OF BIOLOGY   (Russian Federation)

^b INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^c UNIVERSITÉ DE LORRAINE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; CONFERENCE PAPER; CRYSTAL; CRYSTALLOGRAPHY; MACROMOLECULE; MATHEMATICAL ANALYSIS; PHASE TRANSITION; STRUCTURE ANALYSIS;

EID: 0038734402     PISSN: 00442968     EISSN: None     Source Type: Journal    
DOI: 10.1524/zkri.217.12.668.20652     Document Type: Conference Paper

References (61)

1. Anderson, D.; Weiss, M.; Eisenberg, D.: A challenging case for protein structure determination: the mating pheromone Er-1 from Euplotes raikovi. Acta Cryst. D52 (1996) 469-480.
2. Andersson, K. M.; Hovmöller, S.: Phasing Proteins at Low Resolution. Acta Cryst. D52 (1996) 1174-1180.
3. Ævarsson, A.; Braznihnikov, E.; Garber, M.; Zhelnotsova, J.; Chirgadze, Yu.; al-Karadaghi, S.; Svensson, L. A.; Liljas, A.: Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO Journal. 13 (1994) 3669-3677.
4. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. E., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M.: A Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112 (1977) 535-542.
5. Blow, D. M.; Crick, F. H. C.: The Treatment of Errors in the Isomorphous Replacement Method. Acta Cryst. 12 (1959) 794-802.
6. Bricogne, G.; Gilmore, C. J.: A multisolution method of phase determination by combined maximization of entropy and likelihood. I. Theory, algorithms and strategy. Acta Cryst. A46 (1990) 284-297.
7. Carter C. W., Jr.; Crumbley, K. V.; Coleman, D. E.; Hage, F.; Bricogne, G.: Direct Phase Determination for the Molecular Envelope of Tryptophanyl-tRNA Synthetase from Bacillus stearothermophilus by X-ray Contrast Variation. Acta Cryst. A46 (1990) 57-68.
8. Chabriere, E.; Lunina, N.; Lunin, V.Y.; Urzhumtsev, A.: From low resolution to secondary structure elements. ECM-20 Abstracts, XXth European Cryst. Meeting, 25-31 August 2001, Krakow, Poland (2001) 70.
9. Chapman, M. S.; Tsao Jun; Rossmann, M. G.: Ab initio Phase Determination for Spherical Viruses: Parameter Determination for Spherical-Shell Models. Acta Cryst. A48 (1992) 301-312.
10. David, P. R.; Subbiah, S.: Low-Resolution Real-Space Envelopes: the Application of the Condensing-Protocol Approach to the ab initio Macromolecular Phase Problem of a Variety of Examples. Acta Cryst. D50 (1994) 132-138.
11. Derrick, J. P.; Wigley, D. B.: The Third IgG-Binding Domain from Streptococcal Protein G. An Analysis by X-ray Crystallography of the Structure Alone and in a Complex with Fab. J. Mol. Biol. 243 (1994) 906-918.
12. Dorset, D. L.: Low-resolution direct phase determination in protein electron crystallography - breaking globular constraints. Acta Cryst. A56 (2000) 529-535.
13. Gilmore, C. J.: Direct methods and protein crystallography at low resolution. Acta Cryst. D56 (2000) 1205-1214.
14. Guo, D. Y.; Blessing R. H.; Langs, D. A.: Globbic approximation in low-resolution direct-methods phasing. Acta Cryst. D56 (2000) 1148-1155.
15. Chirgadze, Yu.; Nevskaya, N.; Vemoslova, E.; Nikonov, S.; Sergeev, Yu.; Brazhnikov, E.; Fomenkova, N.; Lunin, V. Yu.; Urzhumtsev, A.: Crystal structure of calf eye lens gamma-crystallin IIIb at 2.5A resolution: its relation to function. Exper. Eye Research. 53 (1991) 295-304.
16. Harris, G. W.: Fast ab initio calculation of solvent envelopes for protein structures. Acta Cryst. D51 (1995) 695-702.
17. Harrison, R. W.: Histogram specification as a method of density modification. J. Appl. Cryst. 21 (1988) 949-952.
18. Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M.: Improved method for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47 (1991) 110-119.
19. Lunin, V. Yu.: Use of the information on electron density distribution in macromolecules. Acta Cryst. A44 (1988) 144-150.
20. Lunin, V. Yu.: Electron-denisty histograms and the phase problem. Acta Cryst. D49 (1993) 90-99.
21. Lunin, V. Yu.: Fixed-scale wavelet-type approximation of periodic density distributions. Acta Cryst. A56 (2000) 73-84.
22. Lunin, V. Yu.; Woolfson, M. M.: Mean Phase Error and the Map Correlation Coefficient. Acta Cryst. D49 (1993) 530-533.
23. Lunin, V. Y.; Lunina, N.: The Map Correlation Coefficient for Optimally Superposed Maps. Acta Cryst. A52 (1996) 365-368.
24. Lunin, V. Y.; Urzhumtsev, A.; Skovoroda, T.: Direct low-resolution phasing from electron-density histograms in protein crystallography. Acta Cryst. A46 (1990) 540-544.
25. Lunin, V. Y.; Skovoroda, T.: Frequency-restrained structure-factor refinement. I. Histogram simulation. Acta Cryst. A47 (1991) 45-52.
26. Lunin, V. Y.; Lunina, N.; Petrova, T.; Vemoslova, E.; Urzhumtsev, A.; Podjamy, A. On the ab initio solution of the phase problem for macromolecules at very low resolution: the Few Atoms Model method. Acta Cryst. D51 (1995) 896-903.
27. Lunin, V. Y.; Lunina, N.; Petrova, T.; Urzhumtsev, A.; Podjarny, A.: On the ab initio solution of the phase problem for macromolecules at very low resolution. II. Generalized Likelihood Based Approach to the Cluster Discrimination. Acta Cryst. D54 (1998) 726-734.
28. Lunin, V. Y.; Lunina, N.; Urzhumtsev, A.: Topological properties of high density regions and ab initio phasing at low resolution. Acta Cryst. A56 (2000) 375-382.
29. Lunin, V. Y.; Lunina, N.; Petrova, T.; Skovoroda, T.; Urzhumtsev, A.; Podjamy, A.: Low resolution ab initio phasing. Problems and advances. Acta Cryst. D56 (2000) 1223-1232.
30. Lunin, V. Y.; Lunina, N.; Ritter, S.; Frey, I.; Keul, J.; Diederichs, K.; Podjamy, A.; Urzhumtsev, A.; Baumstark, M.: Low-Resolution Data Analysis for the Low-Density Lipoprotein Particle. Acta Cryst. D57 (2001) 108-121.
31. Lunin, V. Y.; Urzhumtsev, A.; Bockmayr, A.: Direct Phasing by Binary Integer Programming. Acta Cryst. A58 (2002) 283-291.
32. Luzzati, V.; Mariani, P.; Delacroix, H.: X-ray crystallography at macromolecular resolution: a solution of the phase problem. Makromol. Chem. Macromol. Symp. 15 (1988) 1-17.
33. Main, P.; Wilson, J.: Wavelet analysis of electron-density maps. Acta Cryst. D56 (2000) 618-624.
34. Miao, J.; Kirz J.; Sayre D.: The oversampling phasing method. Acta Cryst. D56 (2000) 1312-1315.
35. Miao, J.; Sayre, D.: On possible extensions of X-ray crystallography through diffraction-pattern oversampling. Acta Cryst. A56 (2000) 596-605.
36. Miller, S. T.; Hogle, J. M.; Filman, D. J.: A Genetic Algorithm for the Ab-initio Phasing of Icosahedral Viruses. Acta Cryst. D52 (1996) 235-251.
37. Asp-Aspartyl-tRNA Synthetase: The Crystalline Complex. J. Biomol. Struct. Dynam. 1 (1983) 209-223.
38. Petrova, T.; Lunin, V. Y.; Podjarny, A.: Ab initio low-resolution phasing in crystallography of macromolecules by maximization of likelihood. Acta Cryst. D56 (2000) 1245-1252.
39. Podjarny, A. D.; Rees, B.; Thierry, J.-C.; Cavarelli, J.; Jesior, J. C.; Roth, M.; Lewitt-Bentley, A.; Kahn, R.; Lorber, B.; Ebel, J.-P.; Giegé, R.; Moras, D.: Yeast tRNAAsp-Aspartyl-tRNA Synthetase Complex: Low Resolution Crystal Structure. J. Biomol. Struct. & Dynamics. 5 (1987) 187-198.
40. Ritter, S.; Frey, I.; Diederichs, K.; Grathwohl, D.; Keul, J.; Baumstark, M. W.: Crystallization and Preliminary X-ray Diffraction Data of Two Different Human Low-Density Lipoprotein (LDL) Subfractions Proteins 28 (1997) 293-297.
41. Ritter, S.; Diederichs, K.; Frey, I.; Berg, A.; Keul, J.; Baumstark, M. W.: Crystallization of human low density lipoprotein (LDL), a large lipid-protein complex. Collection of X-ray data at very low resolution. J. Cryst. Growth 196 (1999) 344-349.
42. Sayle, R. A.; Milner-White, E. J.: RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 20 (1995) 374.
43. Service, R. F.: Structural Biology Gets a $150 Million Boost. Science 289 (1994) 2254-2255.
44. Ševcik, J.; Dodson, E.; Dodson, G.: Determination and restrained least-squares refinement of the structures of ribonuclease Sa and its complex with 3′-guanylic acid at 1.8 A resolution Acta Cryst. B47 (1991) 240-253.
45. Shepard, W.; Kahn, R.; Ramin, M.; Fourme, R.: Low-resolution phase information in multiple-wavelength anomalous solvent contrast variation experiments. Acta Cryst. D56 (2000) 1288-1303.
46. Sjölin, L.; Prince, E.; Svenson, L. A.; Gilliland, G. L.: Ab-initio Phase Determination for X-ray Diffraction Data from Crystals of a Native Protein. Acta Cryst. A47 (1991) 216-223.
47. Stark, H.; Mueller, F.; Orlova, E. V.; Schatz, M.; Dube, P.; Erdemir, T.; Zemlin, F.; Brimacombe, R.; van Heel, M.: The 70S Escherichia coli ribosome at 23 Å resolution: fitting the ribosomal RNA. Structure 3 (1995) 815-821.
48. Subbiah, S.: Low-Resolution Real-Space Envelopes: An Approach to the Ab Initio Macromolecular Phase Problem. Science 252 (1991) 128-133.
49. Subbiah, S.: Low-resolution real-space envelopes: improvements to the condensing protocol approach and a new method to fix the sign of such envelopes. Acta Cryst. D49 (1993) 108-119.
50. Tsao, J.; Chapman, M. S.; Rossmann, M. G.: Ab initio Phase Determination for Spherical Viruses: a Feasibility Study. Acta Cryst. A48 (1992) 293-301.
51. Urzhumtsev, A.; Podjarny, A.; Navaza, J.: On the solution of the molecular replacement problem at very low resolution. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 30 (1994) 29-36.
52. Urzhumtsev, A.; Podjarny, A.: On the problem of solvent modelling in macromolecular crystals using diffractional data: 1. The low resolution range. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31 (1995) 12-16.
53. Urzhumtsev, A.; Vernoslova, E.; Podjarny, A.: Approaches to very low resolution phasing of the ribosome 50S particle from Thermus thermophilus by the Few-Atoms-Models and Molecular Replacement methods. Acta Cryst. D52 (1996) 1092-1097.
54. Vernoslova, E. A.; Lunin, V. Yu.: The FROG PC series: programs for electron-density and model investigations for proteins. J. Appl. Cryst. 26 (1993) 291-294.
55. Volkmann, N.: Maximum Entropy, Likelihood and the Large Ribosomal Subunit of Thennus thermophilus. In: Entropy, Likelihood, Bayesian Inference and their Application in Crystal Structure Determination. (Eds. G. Bricogne & C. M. Carter), p. 73-93. ACA, Buffalo, NY 1996.
56. Volkmann, N.; Hottentrager, S.; Hansen, H. A. S.; Zaytsev-Bashan, A.; Sharon, R.; Yonath, A.; Wittmann, H. G.: Characterization and Preliminary Crystallographic Studies on Large Ribosomal Subunits from Thermus thermophilus. J. Mol. Biol. 216 (1990) 239-241.
57. Walser, J. P.: In Proceedings of the Fourteenth National Conference on Artificial Intelligence and Ninth Innovative Applications of Artificial Intelligence Conference, AAAI 97, IAAI 97, July 27-31, 1997, Providence, Rhode Island. AAAI Press/The MIT Press (1997) 269-274.
58. Walser, J. P.: In Proceedings of the Fifteenth National Conference on Artificial Intelligence and Tenth Innovative Applications of Artificial Intelligence Conference, AAAI 98, IAAI 98, July 26-30, 1998, Madison, Wisconsin, USA. AAAI Press/The MIT Press (1998) 373-379.
59. Webster, G.; Hilgenfeld, R.: An evolutionary computational approach to the phase problem in macromolecular X-ray crystallography. Acta Cryst. A57 (2001) 351-358.
60. Wilson, J.; Main, P.: The use of wavelet transforms in low-resolution phase extension. Acta Cryst. D56 (2000) 625-633.
61. Zhang, K. Y. J.; Main, P.: Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A46 (1990) 41-46.